July 10, 2008

Campbell & Tishkoff review paper on African genetic diversity

From the paper:

Several studies of nucleotide and haplotype
variation have indicated that ancestral
African populations were geographically structured
prior to the migration of modern humans
out of Africa (70, 71, 79, 157, 197, 237).
Additionally, a recent study of 800 short tandemrepeat polymorphisms (STRPs) and 400INDELs genotyped in more than 3000 geographicallyand ethnically diverse Africans indicatesthe presence of at least 13 geneticallydistinct ancestral populations in Africa and highlevels of population admixture in many regions
(F.A. Reed & S.A Tishkoff, unpublished data).
Population clusters are correlated with selfdescribed
ethnicity and shared cultural and/or
linguistic properties (e.g., Pygmies, Khoisanspeaking
hunter-gatherers, Bantu speakers,
Cushitic speakers). This study reveals extensiveadmixture between inferred ancestral populationsin most African populations. One exceptionis amongWest African Niger-Kordofanian(i.e., Bantu) speakers who are more geneticallyhomogeneous compared with other Africanpopulations, likely reflecting the recent andrapid spread of Bantu speakers from a commonorigin in Cameroon/Nigeria (although
fine-scale genetic structure can be detected
amongst these populations). Thus, the pattern
of genetic diversity in Africa indicates that
African populations have maintained a large andsubdivided population structure throughoutmuch of their evolutionary history (Figure 2).

As I have argued before, the great genetic diversity of Sub-Saharan Africans is due to the fact that they are composed of several long-differentiated populations admixed with each other. As Figure 2, mentioned above, indicates, NE Africans are related to Eurasians more closely than other Africans, although there has been subsequent gene flow into NE Africans from other Sub-Saharan Africans.
Annual Review of Genomics and Human Genetics
Vol. 9 (Volume publication date September 2008)
(doi:10.1146/annurev.genom.9.081307.164258)
African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping
Michael C. Campbell­, Sarah A. Tishkoff­
Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility.
Link

5 comments:

13 ancestral populations is quite a good number of them, more than could be infered from mtDNA, for instance. It's no surprise, I'll add, that NE Africans (Horners, I assume) are more closely related to Eurasians than any other group.

Autosomal studies seem to yield a too recent picture of groupings. They are complementary certainly, at least when they yield sufficiently deep bayesian K-means analysis, but they can't replace halpid genetics at all.

Overall one of the main problems I've seen in autosomal genetic studies is most visible in PC analysis, where locally important components are just ecclipsed by the overall most sampled ones. This also happens in low depth K-means structure, and maybe even in middle depth one.

In other words, if you are studying a region like West Eurasia and there is, say an specifical Saami component that makes up like 80% of their autosomal structure it's very likely that it won't show up in the continental/subcontinental structure at all, except at pretty deep structure. But very few autosomal studies do that. I have only read one of those that reched K=16 and was about Native Americans. Normally they tend to remain at the surface, what obviously only yields very shallow results.

The structure also varies a lot with samples and recently it's been strongly recommended (this month's PLOS Genetics) to expand samples for better results when possible.

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